bioconductor: DESeq2 | Projects | Ecosyste.ms: Papers

10.1186/s12935-020-01707-9

PPP2R2B downregulation is associated with immune evasion and predicts poor clinical outcomes in triple-negative breast cancer
Cited by: 13
Author(s): Li Zheng, Yaming Li, Xiaolong Wang, Qifeng Yang
Software Mentions: 8
Published: over 4 years ago

10.1186/s12935-020-01661-6

Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development
Cited by: 6
Author(s): R. Adam, Sanne M. van Neerven, Cayetano Pleguezuelos-Manzano, Salvatore Simmini, Nicolas Léveillé, Nina E. de Groot, Andrew N Holding, Florian Markowetz, Louis Vermeulen
Software Mentions: 8
Published: over 4 years ago

10.1186/s13059-020-02072-6

HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis
Cited by: 7
Author(s): Guy Karlebach, Peter J. Hansen, Diogo Veiga, Robin Steinhaus, Daniel Daniš, Sheng Li, Olga Anczuków, Peter N. Robinson
Software Mentions: 8
Published: about 5 years ago

10.7554/eLife.69065

Cross-species analysis defines the conservation of anatomically segregated VMH neuron populations
Cited by: 16
Author(s): Alison H. Affinati, Paul V. Sabatini, Cadence True, Abigail J. Tomlinson, Melissa A. Kirigiti, Sarah R. Lindsley, Chien Li, David P. Olson, Paul Kievit, Martin G. Myers, Alan C. Rupp
Software Mentions: 8
Published: about 4 years ago

10.1186/s13059-021-02261-x

Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer
Cited by: 37
Author(s): Kie Kyon Huang, Jiawen Huang, Jeanie Wu, Ming‐Hui Lee, Su Ting Tay, Vikrant Kumar, R. Kalpana, Nisha Padmanabhan, Chong Xu, Angie Lay Keng Tan, Charlene Chan, Dennis Kappei, Jonathan Göke, Patrick Tan
Software Mentions: 8
Published: over 4 years ago

10.1186/s13059-019-1921-y

Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis
Cited by: 68
Author(s): Rui Yang, Sen Cheng, Nan Luo, Ranran Gao, Kezhuo Yu, Boxi Kang, Li Wang, Qiming Zhang, Fang Qiao, Lei Zhang, Chen Li, Aibin He, Xueda Hu, Jirun Peng, Xianwen Ren, Zemin Zhang
Software Mentions: 8
Published: over 5 years ago

10.3389/fmicb.2021.632935

Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events
Cited by: 19
Author(s): Benjamin Zwirzitz, Stefanie U. Wetzels, Emmanuel D. Dixon, Svenja Fleischmann, Evelyne Selberherr, Sarah Thalguter, Narciso M. Quijada, Monika Dzieciol, Martin Wagner, Beatrix Stessl
Software Mentions: 8
Published: over 4 years ago

10.1038/s41380-020-0844-z

Developmental excitation-inhibition imbalance underlying psychoses revealed by single-cell analyses of discordant twins-derived cerebral organoids
Cited by: 66
Author(s): Tomoyo Sawada, Thomas E. Chater, Yohei Sasagawa, Mika Yoshimura, Noriko Fujimori-Tonou, Kaori Tanaka, Kynon J.M. Benjamin, Apuã C.M. Paquola, Jennifer A. Erwin, Yukiko Goda, Itoshi Nikaido, Takeshi Kato
Software Mentions: 8
Published: almost 5 years ago

10.1371/journal.pgen.1009324

Virus-derived variation in diverse human genomes
Cited by: 0
Author(s): Shohei Kojima, Anselmo Jiro Kamada, Nicholas F. Parrish
Software Mentions: 8
Published: over 4 years ago

10.3389/fmicb.2021.654108

Gut Microbiota of Drosophila subobscura Contributes to Its Heat Tolerance and Is Sensitive to Transient Thermal Stress
Cited by: 22
Author(s): Angélica Jaramillo, Luis E. Castañeda
Software Mentions: 8
Published: about 4 years ago

10.3389/fcimb.2020.00194

Delineation and Modulation of the Natural Killer Cell Transcriptome in Rhesus Macaques During ZIKV and SIV Infections
Cited by: 2
Author(s): Malika Aïd, Daniel R. Ram, Steven E. Bosinger, Dan H. Barouch, R. Keith Reeves
Software Mentions: 8
Published: about 5 years ago

10.1371/journal.pone.0153782

Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools
Cited by: 11
Author(s): Dena Leshkowitz, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, Shirley Horn‐Saban
Software Mentions: 8
Published: over 9 years ago

10.1038/s41598-021-98966-x

Identification of immune-related subtypes of colorectal cancer to improve antitumor immunotherapy
Cited by: 4
Author(s): Xiangkuo Zheng, Yong Gao, Chunhua Yu, Guiquan Fan, Pengwu Li, Ming Zhang, Jian Yu, Mingqing Xu
Software Mentions: 8
Published: almost 4 years ago

10.3389/fgene.2019.00624

Survival Analysis of Multi-Omics Data Identifies Potential Prognostic Markers of Pancreatic Ductal Adenocarcinoma
Cited by: 53
Author(s): Nitish K. Mishra, Siddesh Southekal, Chittibabu Guda
Software Mentions: 8
Published: about 6 years ago

10.1038/s41598-021-93570-5

Three dimensional modeling of biologically relevant fluid shear stress in human renal tubule cells mimics in vivo transcriptional profiles
Cited by: 18
Author(s): Emily J. Ross, Emily R. Gordon, Hanna Sothers, Roshan Darji, Oakley Baron, Dustin W. Haithcock, Balabhaskar Prabhakarpandian, Kapil Pant, R Myers, Sara J. Cooper, Nancy J. Cox
Software Mentions: 8
Published: about 4 years ago

10.1186/s13059-021-02260-y

LINE retrotransposons characterize mammalian tissue-specific and evolutionarily dynamic regulatory regions
Cited by: 31
Author(s): Maša Roller, Ericca L. Stamper, Diego Villar, Osagie Izuogu, Fergal J. Martin, Aisling M. Redmond, Raghavendra Ramachanderan, Louise Harewood, Duncan T. Odom, Paul Flicek
Software Mentions: 8
Published: over 4 years ago

10.3390/v13061019

Human Retrotransposons and the Global Shutdown of Homeostatic Innate Immunity by Oncolytic Parvovirus H-1PV in Pancreatic Cancer
Cited by: 2
Author(s): Matthias Neulinger-Muñoz, Dominik Schaack, Svetlana Grekova, Andrea S. Bauer, Thomas Giese, Gabriel Alexander Salg, Elisa Espinet, Barbara Leuchs, Anette Heller, Jürg P. F. Nüesch, Miriam Schenk, Michael Volkmar, Nathalia A. Giese
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pgen.1009422

High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest
Cited by: 25
Author(s): Seyedeh Masoumeh Fotoukkiaii, Nicky Wybouw, Andre H. Kurlovs, Dimitra Tsakireli, Spiros A. Pergantis, Richard M. Clark, John Vontas, Thomas Van Leeuwen
Software Mentions: 7
Published: about 4 years ago

10.1016/j.cmet.2018.04.013

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes
Cited by: 104
Author(s): Tess Tsai-Hsiu Lu, Steffen Heyne, Erez Dror, Eduard Casas, Laura Leonhardt, Thorina Boenke, Ching‐Yao Yang, Sagar, Laura Arrigoni, Kevin Dalgaard, Raffaele Teperino, Lennart Enders, Madhan Selvaraj, Marius Ruf, Sunil Jayaramaiah Raja, Huafeng Xie, Ulrike Boenisch, Stuart H. Orkin, Francis C. Lynn, Brad G. Hoffman, Dominic Grün, Tanya Vavouri, Adelheid Lempradl, J. Andrew Pospisilik
Software Mentions: 7
Published: about 7 years ago

10.3389/fmicb.2021.660719

Changes in the Community Structure of Under-Ice and Open-Water Microbiomes in Urban Lakes Exposed to Road Salts
Cited by: 14
Author(s): Isabelle B. Fournier, Connie Lovejoy, Warwick F. Vincent
Software Mentions: 7
Published: over 4 years ago

10.1016/j.ccell.2019.08.008

An Evolutionarily Conserved Function of Polycomb Silences the MHC Class I Antigen Presentation Pathway and Enables Immune Evasion in Cancer
Cited by: 314
Author(s): Marian L. Burr, Christina E Sparbier, Kah Lok Chan, Yih-Chih Chan, Ariena Kersbergen, Enid Y.N. Lam, Elizabeth Azidis-Yates, Dane Vassiliadis, Charles C. Bell, Omer Gilan, Susan Jackson, Lavinia Tan, Stephen Q. Wong, Sebastian Hollizeck, Ewa M. Michalak, Hannah V. Siddle, Michael T. McCabe, Rab K. Prinjha, Glen R Guerra, Benjamin Solomon, Shahneen Sandhu, Sarah‐Jane Dawson, Paul A. Beavis, Richard W. Tothill, Carleen Cullinane, Paul J. Lehner, Kate D. Sutherland, Mark A. Dawson
Software Mentions: 7
Published: almost 6 years ago

10.1186/s13059-020-02156-3

STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells
Cited by: 42
Author(s): Tianran Peng, Yanan Zhai, Yaser Atlasi, Menno ter Huurne, Hendrik Marks, Hendrik G. Stunnenberg, Wout Megchelenbrink
Software Mentions: 7
Published: almost 5 years ago

10.3389/fimmu.2020.580373

Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults
Cited by: 13
Author(s): Rym Ben‐Othman, Bing Cai, Aaron C. Liu, Natallia Varankovich, Daniel He, Travis M. Blimkie, Ahwon Lee, Erin E. Gill, M. A. Novotny, Brian D. Aevermann, Sibyl Drissler, Casey P. Shannon, Sarah McCann, Kim Marty, Gordean Bjornson, Rachel D. Edgar, David Lin, Nicole Gladish, Julia L. Maclsaac, Nelly Amenyogbe, Queenie Chan, Alba Llibre, Collin Joyce, Elise Landais, Khoa Le, Samantha M. Reiss, Wayne C. Koff, Colin Havenar-Daughton, Manraj K.S. Heran, Bippan S. Sangha, David R. Walt, Mel Krajden, Shane Crotty, Devin Sok, Bryan Briney, Dennis R. Burton, Darragh Duffy, Leonard J. Foster, William W. Mohn, Michael S. Kobor, Scott J. Tebbutt, Ryan R. Brinkman, Richard H. Scheuermann, Robert E. W. Hancock, Tobias R. Kollmann, Manish Sadarangani
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-021-93918-x

Probiotic supplementation reduces inflammatory profiles but does not prevent oral immune perturbations during SIV infection
Cited by: 4
Author(s): Rhianna Jones, Kyle Kroll, Courtney Broedlow, Luca Schifanella, Scott Smith, Brady Hueber, Spandan V. Shah, Daniel R. Ram, Cordelia Manickam, Valerie Varner, Nichole R. Klatt, R. Keith Reeves
Software Mentions: 7
Published: about 4 years ago

10.1186/s13059-020-1948-0

Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility
Cited by: 42
Author(s): Hyung Joo Lee, Yiran Hou, Yujie Chen, Zea Z. Dailey, Aiyana Riddihough, Hyo Sik Jang, Ting Wang, Stephen L. Johnson
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-020-1930-x

CUBIC: an atlas of genetic architecture promises directed maize improvement
Cited by: 49
Author(s): Haijun Liu, Xiaqing Wang, Yingjie Xiao, Jingyun Luo, Feng Qiao, Wenyu Yang, Ruyang Zhang, Yijiang Meng, Jiamin Sun, Shijuan Yan, Yong Peng, Luyao Niu, Liumei Jian, Wei Song, Jiali Yan, Chunhui Li, Yanxin Zhao, Liu Ya, Marilyn L. Warburton, Jiuran Zhao
Software Mentions: 7
Published: over 5 years ago

10.7554/eLife.69975

Notch-induced endoplasmic reticulum-associated degradation governs mouse thymocyte β−selection
Cited by: 8
Author(s): Xia Liu, Jingjing Yu, Longyong Xu, Katharine Umphred-Wilson, Fanglue Peng, Yao Ding, Brendan M Barton, Xiangdong Lv, Michael Y Zhao, Shengyi Sun, Yuning Hong, Ling Qi, Stanley Adoro, Xi Chen
Software Mentions: 7
Published: about 4 years ago

10.26508/lsa.202000897

Tissue-selective alternate promoters guide NLRP6 expression
Cited by: 1
Author(s): Nathan A. Bracey, Jaye M. Platnich, Arthur Lau, Hyunsoo Chung, M. Eric Hyndman, Justin A. MacDonald, Justin Chun, Paul L. Beck, Stephen E. Girardin, Paul M. Gordon, Daniel A. Muruve
Software Mentions: 7
Published: over 4 years ago

10.3390/life10090185

An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists
Cited by: 3
Author(s): Hamza Mbareche, Nathan Dumont-Leblond, Guillaume J. Bilodeau, Caroline Duchaine
Software Mentions: 7
Published: almost 5 years ago

10.1038/s41419-021-04067-y

Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4
Cited by: 6
Author(s): Thomas Kleiber, Guillaume Davidson, Gabrielle Mengus, Igor Martianov, Irwin Davidson
Software Mentions: 7
Published: almost 4 years ago

10.3390/v13081614

The Repressor C Protein, Pf4r, Controls Superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 Filamentous Phage and Regulates Host Gene Expression
Cited by: 7
Author(s): Muhammad Hafiz Ismail, Katharine A. Michie, Yu Fen Goh, Parisa Noorian, Staffan Kjelleberg, Iain G. Duggin, Diane McDougald, Scott A. Rice
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pgen.1009587

The pluripotent stem cell-specific transcript ESRG is dispensable for human pluripotency
Cited by: 17
Author(s): Kazutoshi Takahashi, Michiko Nakamura, Chikako Okubo, Zane Kliesmete, Mari Ohnuki, Megumi Narita, Akira Watanabe, Mai Ueda, Yasuhiro Takashima, Ines Hellmann, Shinya Yamanaka
Software Mentions: 7
Published: about 4 years ago

10.15252/embj.2020105565

The RNA polymerase II subunit RPB‐9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription
Cited by: 13
Author(s): Ahmet C. Berkyurek, Giulia Furlan, Lisa Lampersberger, Toni Beltran, Eva-Maria Weick, Emily Nischwitz, Isabela Cunha Navarro, Fabian Braukmann, Alper Akay, Jonathan Price, Falk Butter, Peter Sarkies, Eric A. Miska
Software Mentions: 7
Published: over 4 years ago

10.1097/j.pain.0000000000001416

Comprehensive analysis of long noncoding RNA expression in dorsal root ganglion reveals cell-type specificity and dysregulation after nerve injury
Cited by: 41
Author(s): Georgios Baskozos, J. D. K. Dawes, Jean-Sébastien Austin, Ana Antunes-Martins, Lucy A. McDermott, Alex Clark, Teodora Trendafilova, Jon Lees, Stephen B. McMahon, Jeffrey S. Mogil, Christine Orengo, David L.H. Bennett
Software Mentions: 7
Published: almost 7 years ago

10.3390/v13061059

Comparative Analysis of Public RNA-Sequencing Data from Human Intestinal Enteroid (HIEs) Infected with Enteric RNA Viruses Identifies Universal and Virus-Specific Epithelial Responses
Cited by: 5
Author(s): Roberto J. Cieza, Jonathan L. Golob, Justin A. Colacino, Christiane E. Wobus
Software Mentions: 7
Published: about 4 years ago

10.3390/ijms22136726

Analysis of the Role of FRMD5 in the Biology of Papillary Thyroid Carcinoma
Cited by: 4
Author(s): Agata M. Gaweł, Maciej Ratajczak, Ewa Gajda, Małgorzata Grzanka, Agnieszka Paziewska, Marta Cieślicka, Maria Kulecka, Małgorzata Oczko-Wojciechowska, Marlena Godlewska
Software Mentions: 7
Published: about 4 years ago

10.3390/ijms221910451

Differentiation of the High Night Temperature Response in Leaf Segments of Rice Cultivars with Contrasting Tolerance
Cited by: 1
Author(s): Stephanie Schaarschmidt, Ulrike Glaubitz, Alexander Erban, Joachim Kopka, Ellen Zuther
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13059-020-02098-w

Population variation in miRNAs and isomiRs and their impact on human immunity to infection
Cited by: 11
Author(s): Maxime Rotival, Katherine J. Siddle, Martin Silvert, Julien Pothlichet, Hélène Quach, Lluı́s Quintana-Murci
Software Mentions: 7
Published: almost 5 years ago

10.1186/s12931-020-01392-2

Characterisation of microbiota in saliva, bronchoalveolar lavage fluid, non-malignant, peritumoural and tumour tissue in non-small cell lung cancer patients: a cross-sectional clinical trial
Cited by: 27
Author(s): Rea Bingula, Edith Filaire, Ioana Molnar, Eve Delmas, Jean‐Yves Berthon, Marie‐Paule Vasson, Annick Bernalier-Donadille, Marc Filaire
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2020.577474

Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota in vitro, Irrespective of Chemical or Natural Emulsifier Origin
Cited by: 25
Author(s): Lisa Miclotte, Kim De Paepe, Leen Rymenans, Chris Callewaert, Jeroen Raes, Andreja Rajković, John Van Camp, Tom Van de Wiele
Software Mentions: 7
Published: over 4 years ago

10.1242/dev.178590

Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan
Cited by: 13
Author(s): Julien Rougeot, Naomi D. Chrispijn, Marco Aben, Dei M. Elurbe, Karolina M. Andralojc, Patrick J. Murphy, Pascal W.T.C. Jansen, Michiel Vermeulen, Bradley R. Cairns, Leonie M. Kamminga
Software Mentions: 7
Published: over 6 years ago

10.3389/fcimb.2021.733619

Antigen Presenting Cells Link the Female Genital Tract Microbiome to Mucosal Inflammation, With Hormonal Contraception as an Additional Modulator of Inflammatory Signatures
Cited by: 8
Author(s): Elizabeth H. Byrne, M Fărcăşanu, Seth M. Bloom, Nondumiso Xulu, Jiawu Xu, Barry L. Hykes, Nomfuneko A. Mafunda, Matthew R. Hayward, Mary Dong, Krista Dong, Thandeka Gumbi, Fransisca Xolisile Ceasar, Nasreen Ismail, Thumbi Ndung’u, Christina Gosmann, Musie Ghebremichael, Scott A. Handley, Caroline Mitchell, Alexandra Chloé Villani, Douglas S. Kwon
Software Mentions: 7
Published: almost 4 years ago

10.1053/j.gastro.2017.10.007

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome
Cited by: 199
Author(s): Kate J. Howell, Judith Kraiczy, Komal Nayak, Marco Gasparetto, Alex Ross, Claire Lee, Tim N. Mak, Bon–Kyoung Koo, Nitin Kumar, Trevor D. Lawley, Anupam Sinha, Philip Rosenstiel, Robert Heuschkel, Oliver Stegle, Matthias Zilbauer
Software Mentions: 7
Published: over 7 years ago

10.1186/s13059-016-0940-1

A benchmark for RNA-seq quantification pipelines
Cited by: 146
Author(s): Mingxiang Teng, Michael I. Love, Carrie A. Davis, Sarah Djebali, Alexander Dobin, Brenton R. Graveley, Sheng Li, Christopher E. Mason, Sara Olson, Dmitri D. Pervouchine, Cricket A. Sloan, Xintao Wei, Lijun Zhan, Rafael A. Irizarry
Software Mentions: 7
Published: over 9 years ago

10.3389/fimmu.2020.596514

Intestinal Transcriptome Analysis Reveals Soy Derivative-Linked Changes in Atlantic Salmon
Cited by: 26
Author(s): Viswanath Kiron, Youngjin Park, Prabhugouda Siriyappagouder, Dalia Dahle, Ghana Kalerammana Vasanth, Jorge Dias, Jorge M. O. Fernandes, Mette Sørensen, Viviane Verlhac Trichet
Software Mentions: 7
Published: over 4 years ago

10.1016/j.virol.2021.03.019

Zika virus infection during pregnancy protects against secondary infection in the absence of CD8+ cells
Cited by: 3
Author(s): Blake Schouest, Brandon J Beddingfield, Margaret H. Gilbert, Rudolf P. Bohm, Faith Schiro, Pyone P. Aye, Antonito T. Panganiban, Diogo M. Magnani, Nicholas J. Maness
Software Mentions: 7
Published: about 4 years ago

10.1038/s41418-021-00751-w

Bromodomain protein BRDT directs ΔNp63 function and super-enhancer activity in a subset of esophageal squamous cell carcinomas
Cited by: 17
Author(s): Xin Wang, Ana P. Kutschat, Mitsuko Yamada, Evangelos Prokakis, Patricia Böttcher, Koji Tanaka, Yuichiro Doki, Feda H. Hamdan, Steven A. Johnsen
Software Mentions: 7
Published: over 4 years ago

10.7554/eLife.62800

Mapping immune variation and var gene switching in naive hosts infected with Plasmodium falciparum
Cited by: 18
Author(s): Kathryn H. Milne, Alasdair Ivens, Adam J. Reid, Magda E. Lotkowska, Áine O’Toole, Geetha Sankaranarayanan, Diana Muñoz Sandoval, Wiebke Nahrendorf, Clément Regnault, Nick J. Edwards, Sarah E. Silk, Ruth Payne, Angela M. Minassian, Navin Venkatraman, Mandy Sanders, Adrian V. S. Hill, Michael P. Barrett, Matthew Berriman, Simon J. Draper, J. Alexandra Rowe, Philip J. Spence
Software Mentions: 7
Published: over 4 years ago

10.1186/s13059-020-02024-0

Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation
Cited by: 33
Author(s): Mayilaadumveettil Nishana, Caryn Ha, Javier Rodriguez-Hernaez, Ali Ranjbaran, Erica Chio, Elphège P. Nora, Sana Badri, Andreas Kloetgen, Benoit G. Bruneau, Aristotelis Tsirigos, Jane A. Skok
Software Mentions: 7
Published: about 5 years ago

10.1038/s41392-021-00703-3

Differential immune responses in pregnant patients recovered from COVID-19
Cited by: 21
Author(s): Ge Chen, Yiming Zhang, Yaoyao Zhang, Jihui Ai, Bin Yang, Mengge Cui, Qiande Liao, Hanxiao Chen, Hualin Bai, Dashing Shang, Jing Chen, Chaoyang Sun, Haiyi Liu, Fengyuan Liu, Biming Mao, Guoqiang Sun, Lu Chen, Jing-wen Lin, Kezhen Li
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13148-021-01129-y

Differential DNA methylation and changing cell-type proportions as fibrotic stage progresses in NAFLD
Cited by: 22
Author(s): Nicholas Johnson, Xiumei Wu, Christopher D. Still, Xin Chu, Anthony Petrick, Glenn S. Gerhard, Karen N. Conneely, Johanna K. DiStefano
Software Mentions: 7
Published: almost 4 years ago

10.1007/s00572-020-01001-6

Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome
Cited by: 6
Author(s): Christina Paparokidou, Jonathan R. Leake, David J. Beerling, Stephen A. Rolfe
Software Mentions: 7
Published: over 4 years ago

10.1016/j.devcel.2017.07.002

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription
Cited by: 59
Author(s): Alper Akay, Tomás Di Domenico, Kin Man Suen, Amena Nabih, Guillermo E. Parada, Mark Larance, Ragini Medhi, Ahmet C. Berkyurek, Xinlian Zhang, Christopher J. Wedeles, Konrad L. M. Rudolph, Jan Engelhardt, Martin Hemberg, Ping Ma, Angus I. Lamond, Julie M. Claycomb, Eric A. Miska
Software Mentions: 7
Published: almost 8 years ago

10.1186/s13059-020-02144-7

1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding
Cited by: 32
Author(s): Toby Wilkinson, Daniel Korir, Moses Ogugo, Robert D. Stewart, Mick Watson, Edith Paxton, John P. Goopy, Christelle Robert
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0147249

Cell and Microvesicle Urine microRNA Deep Sequencing Profiles from Healthy Individuals: Observations with Potential Impact on Biomarker Studies
Cited by: 43
Author(s): Iddo Z. Ben‐Dov, Veronica M. Whalen, Béatrice Goilav, Klaas E.A. Max, Thomas Tuschl
Software Mentions: 7
Published: over 9 years ago

10.7554/eLife.52511

ERK3/MAPK6 controls IL-8 production and chemotaxis
Cited by: 23
Author(s): Katarzyna Bogucka, Malvika Pompaiah, Fédérico Marini, Harald Binder, Gregory S. Harms, Manuel Kaulich, Matthias Klein, Christian Michel, Markus P. Radsak, Sebastian Rosigkeit, Peter Grimminger, Hansjörg Schild, Krishnaraj Rajalingam
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0219235

Exploring thematic structure and predicted functionality of 16S rRNA amplicon data
Cited by: 17
Author(s): Stephen Woloszynek, Joshua Chang Mell, Zhengqiao Zhao, Gideon Simpson, Michael O’Connor, Gail Rosen
Software Mentions: 7
Published: over 5 years ago

10.1038/s41396-018-0176-z

Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration
Cited by: 64
Author(s): Sylvain Monteux, James T. Weedon, Gesche Blume‐Werry, Konstantin Gavazov, Vincent E. J. Jassey, Margareta Johansson, Frida Keuper, Carolina Olid, Ellen Dorrepaal
Software Mentions: 7
Published: about 7 years ago

10.15252/msb.20209442

High‐throughput, microscope‐based sorting to dissect cellular heterogeneity
Cited by: 40
Author(s): Nicholas Hasle, Anthony Cooke, Sanjay Srivatsan, Heather Z Huang, Jason J. Stephany, Zachary Krieger, Dana L. Jackson, Weiliang Tang, Sriram Pendyala, Raymond J. Monnat, Cole Trapnell, Emily M. Hatch, Douglas M. Fowler
Software Mentions: 7
Published: about 5 years ago

10.3389/fmicb.2018.01620

Rhizosphere Bacterial Communities Differ According to Fertilizer Regimes and Cabbage (Brassica oleracea var. capitata L.) Harvest Time, but Not Aphid Herbivory
Cited by: 26
Author(s): Flora Jane Mary O'Brien, Marc G. Dumont, Jeremy S. Webb, Guy M. Poppy
Software Mentions: 7
Published: about 7 years ago

10.3389/fendo.2021.672319

Adrenocortical Carcinoma Steroid Profiles: In Silico Pan-Cancer Analysis of TCGA Data Uncovers Immunotherapy Targets for Potential Improved Outcomes
Cited by: 6
Author(s): João C. D. Muzzi, Jessica Maria Magno, Milena A. Cardoso, Juliana de Moura, Mauro A. A. Castro, Bonald C. Figueiredo
Software Mentions: 7
Published: about 4 years ago

10.15252/msb.20209652

A substrate‐based ontology for human solute carriers
Cited by: 24
Author(s): Eva Meixner, Ulrich Goldmann, Vitaly Sedlyarov, Stefania Scorzoni, Manuele Rebsamen, Enrico Gottardi, Giulio Superti‐Furga
Software Mentions: 7
Published: about 5 years ago

10.15252/msb.20198831

The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae
Cited by: 40
Author(s): Marco Galardini, Bede P. Busby, Cristina Viéitez, Alistair S. Dunham, Athanasios Typas, Pedro Beltrão
Software Mentions: 7
Published: over 5 years ago

10.1002/cti2.1173

Systematic analysis of the transcriptome in small‐cell carcinoma of the oesophagus reveals its immune microenvironment
Cited by: 2
Author(s): Qi Zhao, Yan‐Xing Chen, Qi‐Nian Wu, Chao Zhang, Min Liu, Yingnan Wang, Yan Feng, Jiajia Hu, Jianhua Fu, Hong Yang, Jingjing Qi, Zixian Wang, Yong Lu, Hui Sheng, Zexian Liu, Zhixiang Zuo, Jian Zheng, Jing‐Ping Yun, Jin‐Xin Bei, Wei‐Hua Jia, Dong Lin, Rui‐Hua Xu, Feng Wang
Software Mentions: 7
Published: over 5 years ago

10.26508/lsa.202101080

Glucocorticoid signaling induces transcriptional memory and universally reversible chromatin changes
Cited by: 9
Author(s): Melissa Bothe, René Buschow, Sebastiaan H. Meijsing
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-020-63565-9

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape
Cited by: 36
Author(s): Bryan Nguyen, Elaine W. Shen, Janina Seemann, Adrienne M. S. Correa, James L. O’Donnell, Andrew H. Altieri, Nancy Knowlton, Keith A. Crandall, Scott P. Egan, W. Owen McMillan, Matthieu Leray
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pgen.1006864

Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder
Cited by: 101
Author(s): Tom S. Koemans, Tjitske Kleefstra, Melissa C. Chubak, Max H. Stone, Margot R.F. Reijnders, Sonja de Munnik, Marjolein H. Willemsen, Michaela Fencková, Connie Stumpel, Levinus A. Bok, Margarita Saenz, Kyna A. Byerly, Linda B. Baughn, Alexander P.A. Stegmann, Rolph Pfundt, Huiqing Zhou, Hans van Bokhoven, Annette Schenck, Jamie M. Kramer
Software Mentions: 7
Published: almost 8 years ago

10.1371/journal.pgen.1008482

A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival
Cited by: 12
Author(s): Rodrigo Guarischi-Sousa, Jhonatas Sirino Monteiro, Lilian Costa Alecrim, Jussara S. Michaloski, Laura Beatriz da Silva Cardeal, Elisa Napolitano Ferreira, Dirce Maria Carraro, Diana Noronha Nunes, Emmanuel Dias-Neto, Jüri Reimand, Paul C. Boutros, João Carlos Setúbal, Ricardo J. Giordano
Software Mentions: 7
Published: over 5 years ago

10.3389/fgene.2019.00662

Cascaded Wx: A Novel Prognosis-Related Feature Selection Framework in Human Lung Adenocarcinoma Transcriptomes
Cited by: 6
Author(s): Bonggun Shin, Sung Soo Park, Ji Hyung Hong, Ho Jung An, Sang Hoon Chun, Kilsoo Kang, Young Ho Ahn, Yoon Ho Ko, Keunsoo Kang
Software Mentions: 7
Published: about 6 years ago

10.1128/mSystems.00280-19

Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition
Cited by: 7
Author(s): Shen Jean Lim, Louie C. Alexander, Annette Summers Engel, Audrey Paterson, Laurie C. Anderson, Barbara J. Campbell
Software Mentions: 7
Published: almost 6 years ago

10.3389/fmicb.2020.607325

Effects of Rare Microbiome Taxa Filtering on Statistical Analysis
Cited by: 53
Author(s): Quy Cao, Xinxin Sun, Karun Rajesh, Naga Chalasani, Kayla Gelow, Barry P. Katz, Vijay H. Shah, Arun J. Sanyal, Ekaterina Smirnova
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pgen.1009763

Deficiency of Polη in Saccharomyces cerevisiae reveals the impact of transcription on damage-induced cohesion
Cited by: 0
Author(s): Pei-Shang Wu, Jan Grosser, Donald P. Cameron, Laura Baranello, Lena Ström
Software Mentions: 7
Published: almost 4 years ago

10.15252/msb.20167507

TT‐seq captures enhancer landscapes immediately after T‐cell stimulation
Cited by: 43
Author(s): Margaux Michel, Carina Demel, Benedikt Zacher, Björn Schwalb, Stefan Krebs, Helmut Blum, Julien Gagneur, Patrick Cramer
Software Mentions: 7
Published: over 8 years ago

10.3389/fimmu.2021.568729

Evolution and Expression of the Immune System of a Facultatively Anadromous Salmonid
Cited by: 7
Author(s): Thomas J. Colgan, Peter Moran, Louise C. Archer, Robert Wynne, Stephen A. Hutton, Philip McGinnity, Thomas E. Reed
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-019-50485-6

Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors
Cited by: 28
Author(s): Sumona P. Dhara, Andrea Rau, Michael J. Flister, Nicole M. Recka, Michael D. Laiosa, Paul L. Auer, Ava J. Udvadia
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pgen.1009331

A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle
Cited by: 20
Author(s): Young Lim Lee, Hitoshi Takeda, Gabriel Costa Monteiro Moreira, Latifa Karim, Erik Mullaart, Wouter Coppieters, Ruth Appeltant, R.F. Veerkamp, Martien A. M. Groenen, Michel Georges, Mirte Bosse, Tom Druet, A.C. Bouwman, Carole Charlier
Software Mentions: 7
Published: about 4 years ago

10.3390/cells10071690

Characterisation of Neurospheres-Derived Cells from Human Olfactory Epithelium
Cited by: 1
Author(s): E. A. Zelenova, Nikolay Kondratyev, Т. В. Лежейко, G. Yu. Tsarapkin, A. I. Kryukov, Alexander E Kishinevsky, A.S. Tovmasyan, Ekaterina Momotyuk, Э. Б. Дашинимаев, В. Е. Голимбет
Software Mentions: 7
Published: about 4 years ago

10.1371/journal.pgen.1009294

Molecular asymmetry in the cephalochordate embryo revealed by single-blastomere transcriptome profiling
Cited by: 4
Author(s): Che-Yi Lin, Mei-Yeh Jade Lu, Jia-Xing Yue, Kun-Lung Li, Yann Le Pétillon, Luok Wen Yong, Yihua Chen, Fu‐Yu Tsai, Yu-Feng Lyu, Cheng-Yi Chen, Sheng-Ping L. Hwang, Yi-Hsien Su, Jr-Kai Yu
Software Mentions: 7
Published: over 4 years ago

10.3389/fimmu.2021.651475

Novel Insights Into Rheumatoid Arthritis Through Characterization of Concordant Changes in DNA Methylation and Gene Expression in Synovial Biopsies of Patients With Differing Numbers of Swollen Joints
Cited by: 5
Author(s): Andrew Y. Li Yim, Enrico Ferrero, Klio Maratou, Huw D. Lewis, George C. Royal, David F. Tough, Chris Larminie, Marcel M.A.M. Mannens, Peter Henneman, Wouter J. de Jonge, Marleen G H van de Sande, Daniëlle M. Gerlag, Rab K. Prinjha, Paul P. Tak
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-021-94343-w

Gene expression analysis method integration and co-expression module detection applied to rare glucide metabolism disorders using ExpHunterSuite
Cited by: 7
Author(s): Fernando M. Jabato, José Córdoba-Caballero, Elena Rojano, Carlos Romá‐Mateo, Pascual Sanz, Belén Pérez, Diana Gallego, Pedro Seoane, Juan A. G. Ranea, James R. Perkins
Software Mentions: 7
Published: about 4 years ago

10.21203/rs.3.rs-438662/v1

Systems biological assessment of human immunity to BNT162b2 mRNA vaccination
Cited by: 2
Author(s): Bali Pulendran, Prabhu S. Arunachalam
Software Mentions: 7
Published: over 4 years ago

10.3389/fimmu.2020.578505

Preparing for Life: Plasma Proteome Changes and Immune System Development During the First Week of Human Life
Cited by: 18
Author(s): Tue Bjerg Bennike, Benoit Fatou, Asimenia Angelidou, Joann Diray‐Arce, Reza Falsafi, Rebecca Ford, Erin E. Gill, Simon D. van Haren, Olubukola T. Idoko, Ahwon Lee, Rym Ben‐Othman, William Pomat, Casey P. Shannon, Kinga K. Smolen, Scott J. Tebbutt, Al Ozonoff, Peter Richmond, Anita H. J. van den Biggelaar, Robert E. W. Hancock, Beate Kampmann, Tobias R. Kollmann, Ofer Levy, Hanno Steen
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0173115

Altered regulation and expression of genes by BET family of proteins in COPD patients
Cited by: 11
Author(s): Rajneesh Malhotra, Nisha Kurian, Xin Zhou, Fang Jiang, Susan J. Monkley, Amy DeMicco, Ib Groth Clausen, Göran Dellgren, Goran Edenro, Miika J. Ahdesmäki, Maryam Clausen, Lisa Öberg, Elisabeth Israelsson, Graham Belfield, Outi Vaarala
Software Mentions: 7
Published: over 8 years ago

10.21203/rs.3.rs-131380/v2

Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets
Cited by: 3
Author(s): Young Il Kim, Kwang-Min Yu, June-Young Koh, Eunha Kim, Se‐Mi Kim, Young Ho Kim, Mark Anthony B. Casel, Rare Rollon, Seung-Gyu Jang, Min‐Suk Song, Su‐Jin Park, Hye Won Jeong, Eung‐Gook Kim, Ok-Jun Lee, Younho Choi, Shin-Ae Lee, Su–Hyung Park, Jae U. Jung, Young Ki Choi
Software Mentions: 7
Published: over 4 years ago

10.1038/s41598-019-52294-3

Oct4-mediated reprogramming induces embryonic-like microRNA expression signatures in human fibroblasts
Cited by: 16
Author(s): Lucie Pešková, Kateřina Černá, Jan Oppelt, Marek Mráz, Tomáš Bárta
Software Mentions: 7
Published: over 5 years ago

10.3389/fimmu.2020.609891

Targeted De-Methylation of the FOXP3-TSDR Is Sufficient to Induce Physiological FOXP3 Expression but Not a Functional Treg Phenotype
Cited by: 26
Author(s): Christopher Kressler, Gilles Gasparoni, Karl Nordström, Dania Hamo, Abdulrahman Salhab, Christoforos Dimitropoulos, Sascha Tierling, Petra Reinke, Hans‐Dieter Volk, Jörn Walter, Alf Hamann, Julia K. Polansky
Software Mentions: 7
Published: over 4 years ago

10.1534/g3.119.0011

Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode Auanema rhodensis
Cited by: 31
Author(s): Sophie Tandonnet, Georgios Koutsovoulos, Sally Adams, Delphine Cloarec, Manish Parihar, Mark Blaxter, André Pires-daSilva
Software Mentions: 7
Published: over 6 years ago

10.1098/rsos.160471

Maternal effects and Symbiodinium community composition drive differential patterns in juvenile survival in the coral Acropora tenuis
Cited by: 55
Author(s): Kate M. Quigley, Bette L. Willis, Line K. Bay
Software Mentions: 7
Published: almost 9 years ago

10.1038/s41598-019-52584-w

Identifying inaccuracies in gene expression estimates from unstranded RNA-seq data
Cited by: 8
Author(s): Mikhail Pomaznoy, Ashu Sethi, Jason A. Greenbaum, Bjoern Peters
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0083984

Characterizing the Infection-Induced Transcriptome of Nasonia vitripennis Reveals a Preponderance of Taxonomically-Restricted Immune Genes
Cited by: 34
Author(s): Timothy B. Sackton, John H. Werren, Andrew G. Clark
Software Mentions: 7
Published: over 11 years ago

10.3389/fimmu.2020.588411

Distinctive Cellular and Metabolic Reprogramming in Porcine Lung Mononuclear Phagocytes Infected With Type 1 PRRSV Strains
Cited by: 6
Author(s): Elisa Crisci, Marco Moroldo, Thien‐Phong Vu Manh, Ammara Mohammad, Laurent Jourdren, Céline Urien, Edwige Bouguyon, Elise Bordet, Claudia Bevilacqua, Mickaël Bourge, Jérémy Pezant, Alexis Pléau, Olivier Boulesteix, Isabelle Schwartz, Nicolas Bertho, Elisabetta Giuffra
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pgen.1008265

Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain
Cited by: 23
Author(s): Aldrin B. Lugena, Ying Zhang, Jérôme S. Menet, Christine Merlin
Software Mentions: 7
Published: about 6 years ago

10.1186/s12920-020-00808-8

Biomarker discovery in attention deficit hyperactivity disorder: RNA sequencing of whole blood in discordant twin and case-controlled cohorts
Cited by: 11
Author(s): Timothy A. McCaffrey, Georges St. Laurent, Dmitry Shtokalo, Денис Антонец, Yuri Vyatkin, Dan Jones, Eleanor Battison, Joel T. Nigg
Software Mentions: 7
Published: over 4 years ago

10.1038/s41419-020-2477-1

Deficiency in the autophagy modulator Dram1 exacerbates pyroptotic cell death of Mycobacteria-infected macrophages
Cited by: 22
Author(s): Rui Zhang, Mónica Varela, Gabriel Forn-Cuní, Vincenzo Torraca, Michiel van der Vaart, Annemarie H. Meijer
Software Mentions: 7
Published: over 5 years ago

10.1016/j.celrep.2019.12.057

Cohesin Disrupts Polycomb-Dependent Chromosome Interactions in Embryonic Stem Cells
Cited by: 118
Author(s): James Rhodes, Angelika Feldmann, Benjamín Hernández-Rodríguez, Noèlia Díaz, Jill M. Brown, Nadezda A. Fursova, Neil P. Blackledge, Praveen Prathapan, Paula Dobrinić, Miles K. Huseyin, Aleksander Szczurek, Kai Kruse, K Nasmyth, Veronica J. Buckle, Juan M. Vaquerizas, Robert J. Klose
Software Mentions: 7
Published: over 5 years ago

10.3389/fimmu.2020.02149

CXCL4 Links Inflammation and Fibrosis by Reprogramming Monocyte-Derived Dendritic Cells in vitro
Cited by: 23
Author(s): Sandra Silva-Cardoso, Weiyang Tao, Chiara Angiolilli, Ana P Lopes, Cornelis P. J. Bekker, Abhinandan Devaprasad, Barbara Giovannone, Jaap van Laar, Marta Cossu, Wioleta Marut, Erik Hack, Rob J. de Boer, Marianne Boes, Timothy R D J Radstake, Aridaman Pandit
Software Mentions: 7
Published: almost 5 years ago

10.1371/journal.pone.0240512

Bone biodeterioration—The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community
Cited by: 19
Author(s): Anne Eriksen, Tue Kjærgaard Nielsen, Henning Matthiesen, Christian Carøe, Lars Hestbjerg Hansen, David Gregory, Gordon Turner‐Walker, Matthew J. Collins, M. Thomas P. Gilbert
Software Mentions: 7
Published: almost 5 years ago

10.1186/s40168-017-0387-y

In-depth resistome analysis by targeted metagenomics
Cited by: 103
Author(s): Val F. Lanza, Fernando Baquero, José Luis Martínez, Ricardo Ramos-Ruíz, Bruno González‐Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, S. Dusko Ehrlich, Sean Kennedy, Étienne Ruppé, Willem van Schaik, Rob J. L. Willems, Fernando de la Cruz, Teresa M. Coque
Software Mentions: 7
Published: over 7 years ago

10.7554/eLife.34031

Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity
Cited by: 39
Author(s): Amy E. Pohodich, Hari Krishna Yalamanchili, Ayush T. Raman, Ying-Wooi Wan, Michael C. Gundry, Shuang Hao, Haijing Jin, Jianrong Tang, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 7
Published: over 7 years ago

10.7554/eLife.30952

Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals
Cited by: 158
Author(s): Inge Kühl, María Miranda, Ilian Atanassov, Irina Kuznetsova, Yvonne Hinze, Arnaud Mourier, Aleksandra Filipovska, Nils‐Göran Larsson
Software Mentions: 7
Published: over 7 years ago

Projects: bioconductor: DESeq2

Enhanced Analysis

Science Score: 100/100

Bonuses:

Papers Mentioning DESeq2 9,583